Overhaul Spack's URL parsing (#2972)

* Remove fake URLs from Spack

* Ignore long lines for URLs that start with ftp:

* Preliminary changes to version regexes

* New redesign of version regexes

* Allow letters in version-only

* Fix detection of versions that end in Final

* Rearrange a few regexes and add examples

* Add tests for common download repositories

* Add test cases for common tarball naming schemes

* Finalize version regexes

* spack url test -> spack url summary

* Clean up comments

* Rearrange suffix checks

* Use query strings for name detection

* Remove no longer necessary url_for_version functions

* Strip off extraneous information after package name

* Add one more test

* Dot in square brackets does not need to be escaped

* Move renaming outside of parse_name_offset

* Fix versions for a couple more packages

* Fix flake8 and doc tests

* Correctly parse Python, Lua, and Bio++ package names

* Use effective URLs for mfem

* Add checksummed version to mitos

* Remove url_for_version from STAR-CCM+ package

* Revert changes to version numbers with underscores and dashes

* Fix name detection for tbb

* Correctly parse Ruby gems

* Reverted mfem back to shortened URLs.

* Updated instructions for better security

* Remove preferred=True from newest version

* Add tests for new `spack url list` flags

* Add tests for strip_name_suffixes

* Add unit tests for version separators

* Fix bugs related to parseable name but in parseable version

* Remove dead code, update docstring

* Ignore 'binary' at end of version string

* Remove platform from version

* Flip libedit version numbers

* Re-support weird NCO alpha/beta versions

* Rebase and remove one new fake URL

* Add / to beginning of regex to avoid picking up similarly named packages

* Ignore weird tar versions

* Fix bug in url parse --spider when no versions found

* Less strict version matching for spack versions

* Don't rename Python packages

* Be a little more selective, version must begin with a digit

* Re-add fake URLs

* Fix up several other packages

* Ignore more file endings

* Add parsing support for Miniconda

* Update tab completion

* XFAILS are now PASSES for 2 web tests

var/spack/repos/builtin/packages/bowtie2/package.py

@@ -29,7 +29,10 @@
 class Bowtie2(Package):
     """Bowtie 2 is an ultrafast and memory-efficient tool for aligning
        sequencing reads to long reference sequences"""
+
     homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
+    url      = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
+
     version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
     version('2.2.5', '51fa97a862d248d7ee660efc1147c75f')
 
@@ -38,10 +41,6 @@ class Bowtie2(Package):
     patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
     patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
 
-    def url_for_version(self, version):
-        url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/{0}/bowtie2-{0}-source.zip"
-        return url.format(version)
-
     def install(self, spec, prefix):
         make()
         mkdirp(prefix.bin)